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Deunan Knute, a young soldier and one of the Global War's last survivors, is rescued by Hitomi, a Second Generation Bioroid. Knute's escape attempt is stopped by her former lover Briareos Hecatonchires, now a cyborg. She realizes that the war had ended and she is in a Utopian city called Olympus. Its population is half-human and half-clone, a genetically-engineered species called Bioroids. Olympus is governed by three factions: Prime Minister Athena Areios; General Edward Uranus III, head of the Olympus Army; and a Council of Elders. Everything in the city is observed by an artificial intelligence named Gaia from a building called Tartaros. While there, Deunan joins the counter-terrorism organization ESWAT.

The Bioroids were created from the DNA of Deunan's father, Carl, making the Second Generation Bioroids her brothers and sisters. However, they have a much shorter lifespan than humans due to suppressed reproductive capabilities. The Bioroid's life extension facilities are destroyed by a secret faction of the Regular Army in a terrorist attack against the Bioroids. However, the Appleseed data, which contains information on restoring the Bioroids reproduction capabilities, still exists.

Olympus is plagued by conflicting factions. Along with a strike force, Deunan and Briareos head to the building where the Bioroids were originally created. She activates a holographic recording showing the location of the Appleseed data. Dr. Gilliam Knute, who created the Bioroids, entrusted Appleseed to Deunan, but was inadvertently killed by a soldier. They are betrayed and cornered by the Regular Army. Deunan discovers from anti-Bioroid terrorist Colonel Hades that Briareos had intentionally allowed his Landmate, a large exoskeleton-like battlesuit, to escape. After Kudoh allowed Deunan and Briareos to escape , he is killed. Uranus attempts to convince Deunan that Bioroids seek to control humanity, and he wants to destroy Appleseed and the D-Tank containing the Bioroid reproductive activation mechanism. Briareos tells Uranus that the Elders manipulated the Army into wanting to destroy the D-Tank, but Athena is trying to prevent them from doing so and protect humanity. Hades, who resents Carl, wounds Briareos only for Deunan to kill him as she and Briareos flee into the sea. Despite Deunan's pleas not to leave Briareos behind, he persuades her to search for the Elders. Mechanic Yoshitsune Miyamoto arrives in his Landmate and begins repairing Briareos after receiving an SOS from him. Deunan flies back to Olympus in Yoshitsune's Landmate and uses the Appleseed data to fully restore Bioroid reproductive functions.

As Deunan encounters the Council of Elders, they reveal their involvement in Gilliam's death and also plan to use the D-tank virus to sterilize humans, which will leave the Bioroids the new rulers of Earth. They needed the Appleseed data to keep the Bioroids alive, but Gilliam hid the data so they could not move forward with their plan. Athena, stepping in to stop them and announcing that Uranus has surrendered, tells Deunan that the Elders had been acting on their own and had shut Gaia down once they realized humanity had softened their stance against Bioroids. The Elders state that they will soon die since Gaia kept them alive, but that they were ready to sacrifice themselves. They then activate the city's mobile fortress defenses, which begin marching towards Tartaros. Athena states that D-tank's security system is nearly impenetrable, but a shot from the fortresses' main cannons might puncture the tank, releasing the virus. ESWAT begins mobilizing, but suffer heavy casualties due to the fortresses' heavy weaponry.

Briareos arrives and asks Deunan to join the battle. Despite the Elders' objections, she goes with him to the towers, and attempts to enter the password to shut the defenses down, but a malfunction makes it difficult. The final password letter appears by itself, and Deunan secures the D-Tank. She reveals that the sins of humanity will probably get worse, but that there is always the chance that future generations will learn from these mistakes; she vows to keep fighting for the children.

The film was released in theaters on April 17, 2004, in Japan. On January 14, 2005, Geneon Entertainment released the film in 30 theaters. It was later released on DVD on May 10, 2005, but with Geneon's name and logo removed from the credits and trailer. Geneon Entertainment's North American division was shut down in December 2007.[2] This allowed the film to be picked up by Sentai Filmworks, with distribution from ADV Films, who re-released it on DVD July 1, 2009.[3] Sentai Filmworks, along with Section23 Films, released Appleseed on Blu-ray Disc on May 18, 2010.[4] The Blu-ray edition of the film includes the original Animaze English dub and an updated dub produced by Seraphim Digital, which features most of the cast from Appleseed Ex Machina. The movie was rereleased in a Blu-ray/DVD set on September 8, 2015, under the Sentai Selects label.[5]

The film has a 24% on Rotten Tomatoes, with critic consensus saying "While visually arresting, Appleseed's narrative and dialogue pondering existentialism is ponderous, awkward, and clumsy."[6] IGN.com gave the film 7 out of 10, commenting that the film is more fun, beautiful and much better than the 1988 film.[7]Anime News Network's Carlo Santos said while the plot is overly cliched, the visual presentation and musical score both stand out and give the film its worth.[8]Helen McCarthy in 500 Essential Anime Movies noted the use of shading and motion capture in the film, stating that "as good as the technology is, the script doesn't match the 1988 version".[9]

Director Shinji Aramaki also directed the sequel to the 2004 movie, titled Appleseed Ex Machina, which was released in October 19, 2007, in Japan. The movie once again featured animated computer-generated imagery, although the cel shaded style was abandoned. In 2014, an indirect prequel titled Appleseed Alpha was announced for a July 22, 2014, release on Blu-ray and DVD after a digital release on July 15, 2014.[10]